List of Abbrevations

Sequences are sent to a category (Pink, Red, Orange, Yellow, Grey) according to their mutation profile. FluWarnSystem counts the amount of mutations in 3 categories:

MOC - Mutation of Concern

Those are mutations that have been identified previously in the literature as changing the potential of the virus. The table of all MOC with their bibliographical reference is at the bottom in the MOC table.

ROI - Region of Interest

Those are important regions of the gene like for example Antigenic sites or Receptor-binding sites. The table of all ROI with their bibliographical reference is at the bottom in the ROI table.

PM - Private Mutation

Mutations that are neither a MOC nor a ROI.

Overview

The report was generated for the following input fasta file:

## > gisaid_epiflu_sequence.fasta

The sequences are from the subtype:

## > Influenza A H1N1pdm

Sequences that are not aligned were skipped because they were thrown out by Nextclade due to errors. For more information, please check the table in the section Skipped Sequences in the QC Report.

## > Sequences total in fasta file: 809
## > Sequences aligned: 802
## > Sequences skipped: 7
## > Metadata was given for the following amount of sequences: 813

Sequences per Group

Group PINK

Sequences with at least 1 MOC and 3 or more MOC & ROI and at least 1 MOC or ROI which is fixed

## > Sequences in Group PINK: 98

Lollipop Plot

Table

Heatmap

Group RED

Sequences with at least 1 MOC and 5 or more MOC & ROI

## > Sequences in Group RED: 0

Lollipop Plot

## No sequences in Group RED

Table

## No sequences in Group RED

Heatmap

## No sequences in Group RED

Group ORANGE

Sequences with at least 1 MOC and 3 or more MOC & ROI

## > Sequences in Group ORANGE: 2

Lollipop Plot

Table

Heatmap

Group YELLOW

Sequences with 0 MOC and 25 or more PM and 7 or less ROI

Sequences with 0 MOC and 8 or more ROI and 24 or less PM

## > Sequences in Group YELLOW: 1

Lollipop Plot

Table

Heatmap

Group GREY

## > Sequences in Group GREY: 701

Reference sequences

The results from this report were calculated with the following reference sequence:

## The Influenza A H1N1pdm reference sequence A/Wisconsin/588/2019 MW626065 was used.

The annotations are generated with Nextclade. The following references are supported for the different Influenza subtypes.

Influenza A H1N1pdm09

For HA segment:

Influenza A H3N2

For HA segment:

Influenza B Victoria

For HA segment:

MOC table

The following table shows a list of the Mutations of Concern that were used to generate the Report.

ROI table

The following table shows a list of Regions of Interest that were used to generate the Report.

Fixed substitutions

The following table shows the fixed mutations for the season, which were excluded from the scoring.